DNA Structure--Study Guide and Lecture Outline

Reminder of DNA’s role in Central Dogma of Biology• What are the functional requirements for a hereditary molecule?• What few organisms use RNA as its hereditary material?

Molecular Structure of DNA• What are Chargaff’s Rules and how did they help other scientists

determine the helical structure of DNA?• What makes up a nucleotide?• What part of the nucleotide distinguishes an “A” nucleotide from a

“G”, or a “C” or a “T”?

Broad course objective: Students will be able toa.) describe the molecular structure of DNA and RNA and indicate similarities and differences; b.) understand the internal structure of DNA strands and how DNA complementary pairing arises

Necessary for future material on:DNA Replication; RNA synthesis, Biotechnology (primers, probes, PCR, Southern and Northern blotting, cloning).

Study guide cont.• Which nucleotides are pyrimidines vs. purines?• What part of the nucleotide makes it function as an “A”

nucleotide for RNA vs. an “A” nucleotide for DNA? Can you use the same nucleotides?

• Within a DNA molecule (or RNA molecule), which bonds are phosphodiester bonds and which are hydrogen bonds? What is the chemical difference? (covalent vs. weak, etc.)

• How many hydrogen bonds are found between G:C pairing vs. A:T pairing?

• What determines whether the end of a DNA strand will be “5 prime” vs. “3 prime”?

• What is a palindrome or hairpin structure?

• I will not be covering the section on B-DNA, A-DNA, and Z-DNA structure.

What makes a good carrier of hereditary information?

• Complex enough to direct the specific expression of many different phenotypes– Traits (macro level)– Proteins (molecular level)

• Transferable to progeny cells or offspring (can be faithfully replicated so that offspring are like parents)

• Allows mutational change proposed by Darwin – Living things do not stay exactly the same generation

after generation, unlike rocks or fire– Living things can evolve and adapt to changes in the

environment

Cellular locations of DNA and RNA

Fig from Audesirk et al., Biology, Life on Earth, 6th ed.

DNA as hereditary material(traditional central dogma)

RNA as hereditary material(retroviruses only)

Historical proof that a nucleic acid--RNA in this case--is the carrier of hereditary information.

• In 1956, A. Gierer and G. Schramm isolated RNA from the tobacco mosaic virus (TMV), a plant virus

Will the progeny viruses be determined by the protein or the nucleic acid?

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or displayBrooker Fig 11.2

Type Rcells

Type Rcells

Type SDNA

extract

Type Rcells

Type SDNA

extract+

DNase

Type Rcells

Type SDNA

extract+

RNase

Type Rcells

Type SDNA

extract+

protease

Transformed Transformed Transformed

DNA is the only molecule that changes the phenotype of recipient cells (survive on limiting growth medium)

No growth

Brooker Figure 11.6Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

DNA structure at various scales

CC

G

AA

GA

TG

GT

T TA

A

GC

AT

AT

T TA

GC

Nucleotides

Single strand

Double helix

Three-dimensional structure

A T CG

CA A

T CA TG

CA

AT C

GC

A

G CA T

Brooker Table 11.1

Base DNA Content of Different Species

HH

H

OCH2

Base

DNA nucleotide

Phosphate

Deoxyribose

HH

OH

OCH2

Base

Phosphate

Ribose

5′

OH OH

4′ 1′

3′ 2′

5′

4′ 1′

3′ 2′

OO

O

P

O–

O

O

P

O–

O

HH HH

Nucleotides of DNA and RNA

Brooker Figure 11.8

RNA nucleotide

Nitrogenous bases of DNA and RNA

Similar to Brooker Figure 11.7

Brooker, Fig 11.17

NH2

N O

N

O

N O

N

Adenine (A)

Guanine (G)

Thymine (T)

BasesBackbone

Cytosine (C)

O

HH

H

H

HH

OOO

O–

P CH2

O–

HH

H

H

H

HH

OOO

O

P CH2

O–

NH2

N

N

H

N

N

HH

H

HH

OOO

O

P CH2

O–

NH2

HN

N

N

H

N

HH

HOH

HH

OOO

O

P CH2

O–Singlenucleotide

Phosphodiesterlinkage

Sugar (deoxyribose)

Phosphate

3′

5′

5′4′ 1′

2′3′

5′4′ 1′

2′3′

5′4′ 1′

2′3′

5′4′ 1′

2′3′

CH3

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Nucleotides are joined at the 5-C and 3-C of each sugar backbone

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or displayBrooker Figure 11.9

Adenosine

Adenosine monophosphate (AMP)

Adenosine diphosphate (ADP)

Adenine

Phosphate groups

Phosphodiester bond

RiboseH

OP CH2

O–

OO P

O–

O O O

–O P

O–

H

OHHO

O

H

2′3

1′4′5′

Adenosine triphosphate (ATP)

NH2

N

H

H

N

NN

Charged nucleotides carry their own energy for the DNA synthesis reaction

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or displayBrooker Fig 11.14

H

N HN

N

N

G

NH2

H

P

S

P

SP

5′ end

3′ end

H NH2

N

N

HH

H

HH

OOO

O

P CH2

O–

HH

H

OH

HH

OOO

O

P CH2

O–

HH

H

HH

OOO

O

P CH2

O–

CH2

HH

H

HH

OOO

O–

P

O–

T

2 nm

2 hydrogen bonds between T and A

TA

G C

T AP

P

P

P

P

S

S

S

S

S

S

S

S

S

A

C

G

C G

C G

G C

G C

GC

G C

C

P

PS

P

P

P

P

P

S

S

S

S

S

PP

P

P

P

P

P

P

P

P

S

S S

S

S

S

S

S

S

P

S

S

P

P

P

S

S

S

S

P

3′

5′

G

S3′5′

S

A

P

P

C

T A

O

N

N

N

NA

H

H NH2

N

O

H

N

CH3

H

T

H

HH2N

N

N C

O

3′ end

5′ end

H

H

HH

OOO

O–

PCH2

O

H

H

H

H

HH

OOO

O–

PCH2

O

H

H

HH

OOO

O–

PCH2

O–

H

H

HH

OOO

O–

PCH2

O

HO

N

O

H

N

CH3

H

T

O

NH N

N

N

G

H2N

H

H

H

N

N

N

N A

H

H2N H

DNA exists in an anti-parallel double helix

3 hydrogen bonds between T and A

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.

Complementary base pairs in DNA

1.) Pyrimidine always pairs with purine

2.) The higher number of hydrogen bonds in GC pairings confer sequence-specific annealing properties

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or displayBrooker, Fig 11.18

Also called hair-pin

Complementary regionsheld together by hydrogen bonds

Noncomplementary regionshave bases projecting away from double-

stranded regions

A U

A U

U A

G C

C G

C G

A U

U A

U A

C G

C G

C G

C G

C G

A

A

U

U

G

G

C

C

C

(a) Bulge loop (b) Internal loop (c) Multibranched junction (d) Stem-loop

G

C

C

G

U

AA

U

G

C

G

C

C

GA

UA U

A U

G C

A U

U A

G C

C G

C G

G

C

G

C

C

GA

U

A

U

G

C

C

G

C

GA

U

A

U

A

U

U

G

G

C

C

CA U

A U

G C

C G

A

AAU

U

U

U

G

G

C

C

Basis of DNA or RNA 2° Structure

ssRNA often forms functional secondary structure

(a) Ribbon model

3′ end(acceptorsite)5′ end

Double helix

Double helix

Anticodon

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

tRNA contains single- and double-stranded regions.

These spontaneously interact to produce 3-D structure.

Brooker Fig 11.19 Anticodon loop

3’ end carries amino acid

tRNA structure

DNA Structure: practice questions

The following comprehension questions (at end of each chapter section) in Brooker, Concepts of Genetics are recommended:• Comprehension Questions (at end of each section): 11.2, 11.3, 11.3, 11.5

#2, 11.7, Answers to Comprehension Questions are at the very end of every chapter.

• Solved Problems at end of chapter (answers included): [none]

• Conceptual questions and Experimental/Application Questions at end of chapter (answers found by logging into publisher’s website, or find them in the book): – Concepts—C1,C4, C5, C7, C8, C13, C14, C17, C20, C25, C26, C27,

C29, E1, – A little more challenging—E3, E9

Go over lecture outline at end of lecture